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- PDB-3e9n: Crystal structure of a putative short-chain dehydrogenase/reducta... -

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Basic information

Entry
Database: PDB / ID: 3e9n
TitleCrystal structure of a putative short-chain dehydrogenase/reductase from Corynebacterium glutamicum
ComponentsPUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASEShort-chain dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dehydrogenases with different specificities (Related to short-chain alcohol dehydrogenases)
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative short-chain dehydrogenase/reductase from Corynebacterium glutamicum
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
B: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
C: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
D: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
E: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
F: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
G: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
H: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE


Theoretical massNumber of molelcules
Total (without water)211,3598
Polymers211,3598
Non-polymers00
Water2,288127
1
A: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
B: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
C: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
D: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE


Theoretical massNumber of molelcules
Total (without water)105,6804
Polymers105,6804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-46 kcal/mol
Surface area28630 Å2
MethodPISA
2
E: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
F: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
G: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE
H: PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE


Theoretical massNumber of molelcules
Total (without water)105,6804
Polymers105,6804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-47 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.107, 62.260, 127.295
Angle α, β, γ (deg.)90.000, 99.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PUTATIVE SHORT-CHAIN DEHYDROGENASE/REDUCTASE / Short-chain dehydrogenase


Mass: 26419.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl2444, cg2685 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NMW9, acetoacetyl-CoA reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6
Details: 100mM MES pH 6.0, 27% PEG MME 5K, 200mM ammonium sulfate, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 2, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.4→29.54 Å / Num. all: 72534 / Num. obs: 72461 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.7 / Num. measured all: 55025 / Num. unique all: 10458 / Rsym value: 0.397 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.77 / SU B: 8.167 / SU ML: 0.195 / SU R Cruickshank DPI: 0.367 / SU Rfree: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.367 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3613 5 %RANDOM
Rwork0.229 ---
obs0.231 72362 99.9 %-
all-72434 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 45.14 Å2 / Biso min: 20.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20.24 Å2
2--0.38 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10752 0 0 127 10879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210902
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9614863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4551446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11424.366426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.375151694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.541567
X-RAY DIFFRACTIONr_chiral_restr0.1070.21845
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218075
X-RAY DIFFRACTIONr_mcbond_it0.8861.57257
X-RAY DIFFRACTIONr_mcangle_it1.689211603
X-RAY DIFFRACTIONr_scbond_it2.61733645
X-RAY DIFFRACTIONr_scangle_it4.4074.53252
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 263 -
Rwork0.241 4959 -
all-5222 -
obs-4959 99.92 %

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